162,742 research outputs found
Where is the bias?
No full textBruggeman, F.J. [Promotor]Gadella, T.W.J. [Promotor]Goedhart, J. [Copromotor
JoachimGoedhart/DataViz-protocols: v0.1
No full textFirst release of the online book "DataViz protocols - An introduction to data visualization protocols for wet lab scientists" by Joachim Goedhart.
Cite as: Goedhart, J. (2022) DataViz protocols - An introduction to data visualization protocols for wet lab scientists, Zenodo, doi: 10.5281/zenodo.645700
Maintenance of memory CD8 T cells: Divided over division
No full textOnce generated during an infection, memory CD8(+) T cells can provide long-lasting protection against reinfection with an intracellular pathogen, but the longevity of this defense depends on the ability of these pathogen-specific memory cells to be maintained. It is generally believed that the bone marrow plays an important role in this respect, where memory CD8 T cells receive reinvigorating signals from cytokines that induce homeostatic proliferation. However, in the current issue of the European Journal of Immunology, Siracusa et al. (Eur. J. Immunol. 2017. 47: 1900-1905) argue against this dogma, as they provide evidence that CD8 memory T cells in murine bone marrow are not proliferating, but largely quiescent, which protects them from elimination by the cytostatic drug Cyclophosphamide. Interestingly, this is in sharp contrast to the proliferating cell counterparts in the spleen, which are eliminated by this treatment. Here, we will discuss the impact of these results, how they relate to opposing findings by others in the field, and what the relevance of these findings is for humans and clinical application
A mTurquoise-based cAMP sensor for both FLIM and ratiometric read-out has improved dynamic range
No full textA mTurquoise-based cAMP sensor for both FLIM and ratiometric read-out has improved dynamic range Klarenbeek, J.B.; Goedhart, J.; Hink, M.A.; Gadella, T.W.J.; Jalink, K. Published in: PLoS ONE DOI: 10.1371/journal.pone.0019170 Link to publication Citation for published version (APA): Klarenbeek, J. B., Goedhart, J., Hink, M. A., Gadella, T. W. J., & Jalink, K. (2011). A mTurquoise-based cAMP sensor for both FLIM and ratiometric read-out has improved dynamic range. PLoS ONE, 6(4), e19170. https://doi.org/10.1371/journal.pone.0019170 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. . Through a conformational change in Epac1, alterations in cellular cAMP levels lead to a change in FRET that is most commonly detected by either Fluorescence Lifetime Imaging (FLIM) or by Sensitized Emission (SE), e.g., by simple ratio-imaging. We recently reported a range of different Epac-based cAMP sensors with high dynamic range and signal-to-noise ratio. We showed that constructs with cyan FP as donor are optimal for readout by SE, whereas other constructs with green FP donors appeared much more suited for FLIM detection. In this study, we present a new cAMP sensor, termed T Epac VV , which employs mTurquoise as donor. Spectrally very similar to CFP, mTurquoise has about doubled quantum efficiency and unlike CFP, its fluorescence decay is strictly singleexponential. We show that T Epac VV appears optimal for detection both by FLIM and SE, that it has outstanding FRET span and signal-to-noise ratio, and improved photostability. Hence, T Epac VV should become the cAMP sensor of choice for new experiments, both for FLIM and ratiometric detection
[Report to Chief J. E. Curry, by an unknown author #1]
No full textReport to Chief J. E. Curry, by an unknown author. The report contains a list of officers who gave depositions to the United States Attorney
[Report to Chief J. E. Curry, by an unknown author #2]
No full textReport to Chief J. E. Curry, by an unknown author. The report contains a list of officers who gave depositions to the United States Attorney
Probing nod factor perception in legumes by fluorescence microspectroscopy
No full textPlants of the family of legumes are capable of forming a symbiosis with Rhizobium bacteria. These Gram-negative bacteria invade the root system of a host legume and fix nitrogen in a specialized organ, the so-called root nodule. In exchange for sugars, the bacteria convert atmospheric nitrogen to ammonia which can be used by the plant. This remarkable alliance allows the plant to grow independently from nitrogen sources provided by the soil. Examples of leguminous plants are clover, pea, and soybean.The symbiosis is initiated by a molecular dialogue. The plant produces flavonoid compounds which are recognized by the bacterial NodD protein. The signaling pathway which is activated leads to the synthesis and secretion of lipo-chitooligosaccharides which are also called Nod factors. The production of Nod factors by the Rhizobium bacteria is an essential step for accomplishing symbiosis and also determines host specificity. The general structure of Nod factors comprises a chitin backbone of three to five b-1,4-linked N-acetylglucosamine units. A fatty acid of 16-20 carbon atoms is N-linked to the terminal non-reducing sugar residue. The exact molecular structure can comprise different acyl chains and a variety of decorations on the chitin backbone depending on the Rhizobium species.After successful recognition of the bacteria by the legume, a remarkable morphogenic process takes place, which is known as root hair curling. The root hair curls around the Rhizobium colony by which the bacteria are entrapped within the so-called shepherd's crook. Subsequently, the rhizobia enter the root hair through an infection thread, starting from the center of the curl. Via the infection thread several cell layers are crossed after which the bacteria are released in nodule primordium cells, where they differentiate into bacteroids that fix nitrogen.Nod factors in the absence of bacteria, either purified from Rhizobium cultures or chemically synthesized can elicit a wide variety of responses on a compatible legume host. When Nod factors are applied to roots, the earliest visible response takes place in root hairs. Root hairs are single tip-growing cells that develop from the epidermis of a root and grow perpendicular from the longitudinal axis of the root. Generally, root hairs that are terminating growth are susceptible to Nod factors and respond by swelling of the tip of the root hairs, followed by the re-initiation of tip growth in a random direction. This typical Nod factor response is referred to as root hair deformation and can be observed with a microscope 2-3 hours after addition of Nod factors.The perception of Nod factors by the plant, and the downstream signaling cascades that are activated are major research topics in the Rhizobium-legume interaction. The low concentration (down to 10-12 M) at which Nod factors can still induce root hair deformation and the dependence of the bioactivity on specific decorations of the Nod factor suggest that these molecules are perceived by receptors at the root hair. However, to date no such receptors are characterized. Moreover, it is far from clear where Nod factor recognition by root hairs takes place. Therefore an approach was taken in which fluorescent Nod factor derivatives are synthesized, allowing to probe the ligand binding sites on legume root hairs.The research described in this thesis focuses on the quantification, characterization and perception by legumes of Nod factors. In order to detect Nod factors at physiologically relevant concentrations sensitive techniques are required. A number of fluorescence spectroscopy and microscopy based techniques can be used to study fluorescent derivatives of signaling molecules. In chapter 1, the use of fluorescence microspectroscopic techniques available in the laboratory are discussed. Examples how these techniques can be used for the study of root hairs and other living cells are described.In chapter 2, two methods to quantify purified Nod factors are described. An enzymatic step which is crucial for the first method was analyzed in detail. The second method was optimized and validated using fluorescent and radiolabeled Nod factor derivatives. The chapter describes in detail how the two optimized methods can be used for quantifying Nod factors as well as potential pitfalls.In chapter 3, the spectral properties of three novel fluorescent Nod factor derivatives are described. It is checked whether these fluorescent Nod factors can still elicit root hair deformation on Vicia sativa roots. The properties of the amphiphilic signaling molecules were characterized in vitro in the absence and presence of micelles and model membrane systems using fluorescence spectroscopy. Time-correlated single photon counting fluorescence spectroscopy was used to measure rotational mobility of the fluorophore. These experiments are complemented with fluorescence correlation spectroscopy to examine diffusional mobility of the Nod factors. A lipid transfer assay was used to measure the rate of intermembrane transfer and intramembrane flip-flop of Nod factors.In chapter 4, a detailed study is reported describing the sites at which the fluorescent Nod factors accumulate. Fluorescence microscopy is used to examine the location of fluorescent Nod factors on root hairs during the initial perception and during root hair deformation. Subsequently, the diffusional mobility of the fluorescent Nod factors is measured in vivo using fluorescence correlation microscopy (FCM), allowing quantification of molecular mobility and concentration of fluorescent Nod factors in living root hairs at a molecular level. This study is continued in chapter 5 in which also novel sulfated fluorescent Nod factors are used and characterized, enabling a direct comparison between sulfated and non-sulfated Nod factors on a host and non-host legume. Also, the origin of the molecular mobility of the Nod factors is studied in more detail.In chapter 6 a novel approach towards manipulating phospholipid second messengers in single cells with spatiotemporal control is presented. The synthesis of a fluorescent and caged derivative, NPE-phosphatidic acid, which releases phosphatidic acid upon exposure to UV is described. The release of phosphatidic acid from the caged compound is studied in vitro and in vivo. The use of photoreleasable phosphatidic acid for studying phospholipid signaling in vivo is evaluated.Chapter 7 summarizes the conclusions that can be drawn from the results described in this thesis. The implications for Nod factor secretion by the bacterium and subsequent perception by legume root hairs are discussed. Based on the results presented in this thesis, it is tempting to speculate that spatial restriction of signaling molecules in plants is achieved by immobilization in the cell wall. Subseqent perception of Nod factor takes place either in the plasma membrane or within the cell wall as is illustrated by two proposed modes of perception. The results of this thesis are discussed with respect to these two models.</p
Material related to the blog that reports on the parrot LUT
No full textMaterial related to the blog that reports on the parrot LUT
The blog was published at the Node: http://thenode.biologists.com/parrot-lut/research/
-Source
The ‘morgenstemning’ LUT was originally described in:
M. Geissbuehler and T. Lasser - "How to display data by color schemes compatible with red-green color perception deficiencies”, Optics Express, 2013
The ‘inferno’ LUT was originally created by Stéfan van der Walt and Nathaniel Smith (http://bids.github.io/colormap/).
The ‘pseudocolorMM’ LUT was derived from MetaMorph software (version 7.6).
The ‘royal’ and ‘Fire’ LUT are available in ImageJ (version 1.49j)
The ‘parrot’ LUT was designed by Joachim Goedhart and first described here:
http://thenode.biologists.com/parrot-lut/research/
-Distribution
The colormaps Magma, Inferno, Plasma and Viridis are available under a CC0 "no rights reserved" license (https://creativecommons.org/share-your-work/public-domain/cc0) and are present in FIJI.
The colormaps Mongenstemning & Parrot are free software: you can redistribute them and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
These colormaps are distributed in the hope that they will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details: http://www.gnu.org/licenses/>.</p
Murder on the mountain: author talk with Peter J. Wosh
No full textAuthor talk by Peter J. Wosh on May 5th, 2022, on his book, "Murder on the Mountain: crime, passion, and punishment in gilded age New Jersey.
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